chr10-133230834-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003577.3(UTF1):c.546A>T(p.Glu182Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00144 in 1,302,268 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003577.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UTF1 | NM_003577.3 | c.546A>T | p.Glu182Asp | missense_variant | 1/2 | ENST00000304477.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UTF1 | ENST00000304477.3 | c.546A>T | p.Glu182Asp | missense_variant | 1/2 | 1 | NM_003577.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000885 AC: 134AN: 151392Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00256 AC: 3AN: 1174Hom.: 0 AF XY: 0.00257 AC XY: 2AN XY: 778
GnomAD4 exome AF: 0.00152 AC: 1745AN: 1150768Hom.: 0 Cov.: 35 AF XY: 0.00150 AC XY: 837AN XY: 556278
GnomAD4 genome ? AF: 0.000884 AC: 134AN: 151500Hom.: 0 Cov.: 33 AF XY: 0.000743 AC XY: 55AN XY: 74064
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 13, 2021 | The c.546A>T (p.E182D) alteration is located in exon 1 (coding exon 1) of the UTF1 gene. This alteration results from a A to T substitution at nucleotide position 546, causing the glutamic acid (E) at amino acid position 182 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at